Variant report

Variant	rs2453595
Chromosome Location	chr17:19483855-19483856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:19483602-19484254	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000228983	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10735	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120272	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120273	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2249885	0.95[EUR][1000 genomes]
rs2440167	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453596	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212622	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2453595	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2453595	CTD-2104P17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19481200-19485600	Weak transcription	HepG2	liver
2	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr17:19482600-19484000	Bivalent Enhancer	Placenta	Placenta
5	chr17:19482800-19484000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:19482800-19484000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr17:19482800-19484000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:19482800-19484000	Active TSS	Brain Germinal Matrix	brain
9	chr17:19483000-19484000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:19483000-19484000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr17:19483000-19484200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
12	chr17:19483200-19484000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:19483200-19484000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
14	chr17:19483400-19484000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:19483400-19484000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr17:19483400-19484000	Active TSS	Brain Angular Gyrus	brain
17	chr17:19483400-19484000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr17:19483600-19484000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr17:19483600-19484000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr17:19483600-19484000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr17:19483600-19484000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr17:19483600-19484000	Bivalent Enhancer	Lung	lung
23	chr17:19483600-19484000	Flanking Active TSS	Ovary	ovary
24	chr17:19483600-19484200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
25	chr17:19483800-19484000	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:19483800-19484000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:19483800-19484000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr17:19483800-19484000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr17:19483800-19484000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:19483800-19484000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:19483800-19484000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:19483800-19484000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:19483800-19484000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:19483800-19484000	Enhancers	Colon Smooth Muscle	Colon
35	chr17:19483800-19484000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
36	chr17:19483800-19484000	Enhancers	Fetal Brain Male	brain
37	chr17:19483800-19484000	Bivalent Enhancer	Fetal Intestine Large	intestine
38	chr17:19483800-19484000	Bivalent Enhancer	Fetal Lung	lung
39	chr17:19483800-19484000	Bivalent Enhancer	Fetal Stomach	stomach
40	chr17:19483800-19484000	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links